#include <LayerDesignOperation.hh>

Inheritance diagram for protocols::flxbb::LayerDesignOperation:

Collaboration diagram for protocols::flxbb::LayerDesignOperation:

Public Types
typedef std::string	String

typedef core::Real	Real

typedef core::pose::Pose	Pose

typedef core::pack::task::PackerTask	PackerTask

typedef core::pack::task::operation::TaskOperation	TaskOperation

typedef core::pack::task::operation::TaskOperationOP	TaskOperationOP

typedef TaskOperation	parent

typedef utility::tag::TagPtr	TagPtr

typedef std::map< std::string, TaskOperationOP >	TaskLayers

typedef std::pair< std::string, TaskOperationOP >	TaskLayer

typedef std::map< std::string, std::string >	LayerDefinitions

typedef std::pair< std::string, std::string >	LayerDefinition

typedef std::map< std::string, LayerDefinitions >	LayerResidues

typedef std::pair< std::string, LayerDefinitions >	Layer

Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagPtr	TagPtr

typedef pose::Pose	Pose

Public Member Functions
	LayerDesignOperation ()
	default constructor More...

	LayerDesignOperation (bool dsgn_core, bool dsgn_boundary, bool dsgn_surface)
	value constructor More...

virtual	~LayerDesignOperation ()
	destructor More...

virtual TaskOperationOP	clone () const
	make clone More...

void	design_layer (bool const dsgn_core, bool const dsgn_boundary, bool const dsgn_surface)
	layer to be designed More...

void	sasa_surface (Real const r, String const ss="")
	accessible surface for evaluating residues are in surface or not More...

void	sasa_core (Real const r, String const ss="")
	accessible surface for evaluating residues are in core or not More...

void	pore_radius (Real ps)
	set pore radius for colculating asa More...

void	set_verbose (bool const b)
	set verbose More...

void	set_restrict_restypes (bool const b)
	set restrict_restypes More...

void	use_original_seq ()
	use original sequence for not designed layer More...

void	make_pymol_script (bool value)
	make pymol scripts showing the different layers More...

void	parse_tag (TagPtr tag)
	Used to parse an xml-like tag to load parameters and properties. More...

virtual void	apply (Pose const &pose, PackerTask &task) const
	apply More...

Public Member Functions inherited from core::pack::task::operation::TaskOperation
virtual	~TaskOperation ()

virtual void	parse_def (utility::lua::LuaObject const &def)

Private Member Functions
utility::vector1< bool >	get_restrictions (std::string const &layer, std::string const &default_layer, std::string const &ss_type) const

void	set_default_layer_residues ()

std::string	pos2select (utility::vector1< Size > const &pos) const
	utility function to transform a vector of position into a pymol selection command More...

void	write_pymol_script (Pose const &pos, toolbox::SelectResiduesByLayerOP srbl, std::map< std::string, utility::vector1< bool > > const &layer_specification, bool las_ligand, std::string const &filename) const
	write a pymol command with the different layers as selections More...

Private Attributes
bool	add_helix_capping_
	add helix capping ? More...

bool	use_original_
	use original sequence for not designed layer ? More...

bool	repack_non_designed_residues_

bool	verbose_

bool	restrict_restypes_

bool	make_pymol_script_

LayerResidues	layer_residues_

std::map< std::string, bool >	design_layer_

TaskLayers	task_layers_

toolbox::SelectResiduesByLayerOP	srbl_

Member Typedef Documentation

typedef std::pair< std::string, LayerDefinitions > protocols::flxbb::LayerDesignOperation::Layer

typedef std::pair< std::string, std::string > protocols::flxbb::LayerDesignOperation::LayerDefinition

typedef std::map< std::string, std::string > protocols::flxbb::LayerDesignOperation::LayerDefinitions

typedef std::map< std::string, LayerDefinitions > protocols::flxbb::LayerDesignOperation::LayerResidues

typedef core::pack::task::PackerTask protocols::flxbb::LayerDesignOperation::PackerTask

typedef TaskOperation protocols::flxbb::LayerDesignOperation::parent

typedef core::pose::Pose protocols::flxbb::LayerDesignOperation::Pose

typedef core::Real protocols::flxbb::LayerDesignOperation::Real

typedef std::string protocols::flxbb::LayerDesignOperation::String

typedef utility::tag::TagPtr protocols::flxbb::LayerDesignOperation::TagPtr

typedef std::pair< std::string, TaskOperationOP > protocols::flxbb::LayerDesignOperation::TaskLayer

typedef std::map< std::string, TaskOperationOP > protocols::flxbb::LayerDesignOperation::TaskLayers

typedef core::pack::task::operation::TaskOperation protocols::flxbb::LayerDesignOperation::TaskOperation

typedef core::pack::task::operation::TaskOperationOP protocols::flxbb::LayerDesignOperation::TaskOperationOP

Constructor & Destructor Documentation

protocols::flxbb::LayerDesignOperation::LayerDesignOperation ( )

default constructor

References set_default_layer_residues().

Referenced by clone().

protocols::flxbb::LayerDesignOperation::LayerDesignOperation	(	bool	dsgn_core,
		bool	dsgn_boundary,
		bool	dsgn_surface
	)

value constructor

References design_layer(), and set_default_layer_residues().

protocols::flxbb::LayerDesignOperation::~LayerDesignOperation ( )

virtual

destructor

Member Function Documentation

void protocols::flxbb::LayerDesignOperation::apply	(	Pose const &	pose,
		PackerTask &	task
	)		const

virtual

apply

Implements core::pack::task::operation::TaskOperation.

References add_helix_capping_, core::pack::task::ResidueLevelTask::command_string(), design_layer_, core::pack::task::PackerTask_::designing_residues(), core::scoring::dssp::Dssp::dssp_reduced(), core::pose::symmetry::extract_asymmetric_unit(), protocols::swa::rna::file_exists(), protocols::flxbb::find_ligands(), core::scoring::dssp::Dssp::get_dssp_secstruct(), get_restrictions(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), make_pymol_script_, core::pack::task::PackerTask::nonconst_residue_task(), core::pack::task::ResidueLevelTask::prevent_repacking(), repack_non_designed_residues_, core::pose::Pose::residue(), core::pack::task::PackerTask::residue_task(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), core::pack::task::ResidueLevelTask::restrict_to_repacking(), srbl_, task_layers_, core::pose::Pose::total_residue(), protocols::TR(), verbose_, and write_pymol_script().

core::pack::task::operation::TaskOperationOP protocols::flxbb::LayerDesignOperation::clone ( ) const

virtual

make clone

clone

Implements core::pack::task::operation::TaskOperation.

References LayerDesignOperation().

void protocols::flxbb::LayerDesignOperation::design_layer	(	bool const	dsgn_core,
		bool const	dsgn_boundary,
		bool const	dsgn_surface
	)

layer to be designed

References srbl_.

Referenced by LayerDesignOperation().

utility::vector1< bool > protocols::flxbb::LayerDesignOperation::get_restrictions	(	std::string const &	layer,
		std::string const &	default_layer,
		std::string const &	ss_type
	)		const

private

References core::chemical::aa_from_oneletter_code(), layer_residues_, and core::chemical::num_canonical_aas.

Referenced by apply().

void protocols::flxbb::LayerDesignOperation::make_pymol_script ( bool value)

inline

make pymol scripts showing the different layers

Referenced by parse_tag().

void protocols::flxbb::LayerDesignOperation::parse_tag ( TagPtr tag)

virtual

Used to parse an xml-like tag to load parameters and properties.

Reimplemented from core::pack::task::operation::TaskOperation.

References design_layer_, core::pack::task::operation::TaskOperationFactory::get_instance(), core::pack::task::operation::TaskOperationFactory::has_type(), layer_residues_, make_pymol_script(), core::pack::task::operation::TaskOperationFactory::newTaskOperation(), repack_non_designed_residues_, set_restrict_restypes(), set_verbose(), srbl_, task_layers_, protocols::TR(), and use_original_.

void protocols::flxbb::LayerDesignOperation::pore_radius ( Real ps)

set pore radius for colculating asa

References srbl_.

std::string protocols::flxbb::LayerDesignOperation::pos2select ( utility::vector1< Size > const & pos) const

private

utility function to transform a vector of position into a pymol selection command

References protocols::kinmatch::str().

Referenced by write_pymol_script().

void protocols::flxbb::LayerDesignOperation::sasa_core	(	Real const	r,
		String const	ss = `""`
	)

accessible surface for evaluating residues are in core or not

References srbl_.

void protocols::flxbb::LayerDesignOperation::sasa_surface	(	Real const	r,
		String const	ss = `""`
	)

accessible surface for evaluating residues are in surface or not

References srbl_.

void protocols::flxbb::LayerDesignOperation::set_default_layer_residues ( )

private

References design_layer_, protocols::simple_moves::insert, layer_residues_, and protocols::TR().

Referenced by LayerDesignOperation().

void protocols::flxbb::LayerDesignOperation::set_restrict_restypes ( bool const b)

inline

set restrict_restypes

References protocols::match::upstream::b.

Referenced by parse_tag().

void protocols::flxbb::LayerDesignOperation::set_verbose ( bool const b)

inline

set verbose

References protocols::match::upstream::b.

Referenced by parse_tag().

void protocols::flxbb::LayerDesignOperation::use_original_seq ( )

inline

use original sequence for not designed layer

void protocols::flxbb::LayerDesignOperation::write_pymol_script	(	Pose const &	pos,
		toolbox::SelectResiduesByLayerOP	srbl,
		std::map< std::string, utility::vector1< bool > > const &	layer_specification,
		bool	las_ligand,
		std::string const &	filename
	)		const

private

write a pymol command with the different layers as selections

References core::pose::Pose::dump_pdb(), pos2select(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by apply().

Member Data Documentation

bool protocols::flxbb::LayerDesignOperation::add_helix_capping_

private

add helix capping ?

Referenced by apply().

std::map< std::string, bool > protocols::flxbb::LayerDesignOperation::design_layer_

private

Referenced by apply(), parse_tag(), and set_default_layer_residues().

LayerResidues protocols::flxbb::LayerDesignOperation::layer_residues_

private

Referenced by get_restrictions(), parse_tag(), and set_default_layer_residues().

bool protocols::flxbb::LayerDesignOperation::make_pymol_script_

private

Referenced by apply().

bool protocols::flxbb::LayerDesignOperation::repack_non_designed_residues_

private

Referenced by apply(), and parse_tag().

bool protocols::flxbb::LayerDesignOperation::restrict_restypes_

private

toolbox::SelectResiduesByLayerOP protocols::flxbb::LayerDesignOperation::srbl_

private

Referenced by apply(), design_layer(), parse_tag(), pore_radius(), sasa_core(), and sasa_surface().

TaskLayers protocols::flxbb::LayerDesignOperation::task_layers_

private

Referenced by apply(), and parse_tag().

bool protocols::flxbb::LayerDesignOperation::use_original_

private

use original sequence for not designed layer ?

Referenced by parse_tag().

bool protocols::flxbb::LayerDesignOperation::verbose_

private

Referenced by apply().

The documentation for this class was generated from the following files:

src/protocols/flxbb/LayerDesignOperation.hh
src/protocols/flxbb/LayerDesignOperation.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation